[2023-06-28 15:27:16,301] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:27:16,303] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:27:16,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b9558d8-e45e-46cc-9338-b1cc6462827c/dqc_reference
[2023-06-28 15:27:17,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:27:17,448] [INFO] Task started: Prodigal
[2023-06-28 15:27:17,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg319c9514-31fc-4f89-afd3-5dc27b920b26/GCA_017986355.1_ASM1798635v1_genomic.fna.gz | prodigal -d GCA_017986355.1_ASM1798635v1_genomic.fna/cds.fna -a GCA_017986355.1_ASM1798635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:27:27,384] [INFO] Task succeeded: Prodigal
[2023-06-28 15:27:27,385] [INFO] Task started: HMMsearch
[2023-06-28 15:27:27,385] [INFO] Running command: hmmsearch --tblout GCA_017986355.1_ASM1798635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b9558d8-e45e-46cc-9338-b1cc6462827c/dqc_reference/reference_markers.hmm GCA_017986355.1_ASM1798635v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:27:27,559] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:27:27,560] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg319c9514-31fc-4f89-afd3-5dc27b920b26/GCA_017986355.1_ASM1798635v1_genomic.fna.gz]
[2023-06-28 15:27:27,582] [INFO] Query marker FASTA was written to GCA_017986355.1_ASM1798635v1_genomic.fna/markers.fasta
[2023-06-28 15:27:27,582] [INFO] Task started: Blastn
[2023-06-28 15:27:27,583] [INFO] Running command: blastn -query GCA_017986355.1_ASM1798635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b9558d8-e45e-46cc-9338-b1cc6462827c/dqc_reference/reference_markers.fasta -out GCA_017986355.1_ASM1798635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:27:28,197] [INFO] Task succeeded: Blastn
[2023-06-28 15:27:28,201] [INFO] Selected 18 target genomes.
[2023-06-28 15:27:28,202] [INFO] Target genome list was writen to GCA_017986355.1_ASM1798635v1_genomic.fna/target_genomes.txt
[2023-06-28 15:27:28,202] [INFO] Task started: fastANI
[2023-06-28 15:27:28,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg319c9514-31fc-4f89-afd3-5dc27b920b26/GCA_017986355.1_ASM1798635v1_genomic.fna.gz --refList GCA_017986355.1_ASM1798635v1_genomic.fna/target_genomes.txt --output GCA_017986355.1_ASM1798635v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:27:41,432] [INFO] Task succeeded: fastANI
[2023-06-28 15:27:41,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b9558d8-e45e-46cc-9338-b1cc6462827c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:27:41,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b9558d8-e45e-46cc-9338-b1cc6462827c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:27:41,447] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 15:27:41,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 15:27:41,448] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Bacteroides graminisolvens	strain=DSM 19988	GCA_000428125.1	477666	477666	type	True	98.7831	612	642	95	conclusive
Bacteroides graminisolvens	strain=JCM 15093	GCA_000613825.1	477666	477666	type	True	98.7609	617	642	95	conclusive
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	79.3218	111	642	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	78.6197	142	642	95	below_threshold
Bacteroides ihuae	strain=Marseille-P2824	GCA_900104585.1	1852362	1852362	type	True	78.1619	210	642	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.1333	109	642	95	below_threshold
Bacteroides neonati	strain=MS4	GCA_000499785.1	1347393	1347393	type	True	78.0143	115	642	95	below_threshold
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	77.8295	113	642	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	77.7217	110	642	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	77.6651	131	642	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	77.6028	138	642	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	77.5731	132	642	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	77.5362	129	642	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	77.5147	142	642	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	77.5018	142	642	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	77.4247	123	642	95	below_threshold
Bacteroides reticulotermitis	strain=DSM 105720	GCA_014196955.1	1133319	1133319	type	True	77.4047	112	642	95	below_threshold
Bacteroides reticulotermitis	strain=JCM 10512	GCA_000517545.1	1133319	1133319	type	True	77.3949	109	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:27:41,450] [INFO] DFAST Taxonomy check result was written to GCA_017986355.1_ASM1798635v1_genomic.fna/tc_result.tsv
[2023-06-28 15:27:41,450] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:27:41,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:27:41,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b9558d8-e45e-46cc-9338-b1cc6462827c/dqc_reference/checkm_data
[2023-06-28 15:27:41,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:27:41,475] [INFO] Task started: CheckM
[2023-06-28 15:27:41,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017986355.1_ASM1798635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017986355.1_ASM1798635v1_genomic.fna/checkm_input GCA_017986355.1_ASM1798635v1_genomic.fna/checkm_result
[2023-06-28 15:28:14,138] [INFO] Task succeeded: CheckM
[2023-06-28 15:28:14,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:28:14,156] [INFO] ===== Completeness check finished =====
[2023-06-28 15:28:14,156] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:28:14,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017986355.1_ASM1798635v1_genomic.fna/markers.fasta)
[2023-06-28 15:28:14,157] [INFO] Task started: Blastn
[2023-06-28 15:28:14,157] [INFO] Running command: blastn -query GCA_017986355.1_ASM1798635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b9558d8-e45e-46cc-9338-b1cc6462827c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017986355.1_ASM1798635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:28:14,948] [INFO] Task succeeded: Blastn
[2023-06-28 15:28:14,957] [INFO] Selected 18 target genomes.
[2023-06-28 15:28:14,957] [INFO] Target genome list was writen to GCA_017986355.1_ASM1798635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:28:14,959] [INFO] Task started: fastANI
[2023-06-28 15:28:14,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg319c9514-31fc-4f89-afd3-5dc27b920b26/GCA_017986355.1_ASM1798635v1_genomic.fna.gz --refList GCA_017986355.1_ASM1798635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017986355.1_ASM1798635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:28:27,297] [INFO] Task succeeded: fastANI
[2023-06-28 15:28:27,311] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:28:27,311] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000428125.1	s__Bacteroides graminisolvens	98.7831	612	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	97.75	0.90	0.81	13	conclusive
GCF_000011065.1	s__Bacteroides thetaiotaomicron	78.6312	141	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_900104585.1	s__Bacteroides ihuae	78.1619	210	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000499785.1	s__Bacteroides neonati	78.0076	116	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000381365.1	s__Bacteroides salyersiae	77.9572	117	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_002849695.1	s__Bacteroides fragilis_A	77.8099	137	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCA_002307035.1	s__Bacteroides sp002307035	77.7364	187	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.69	98.69	0.85	0.85	2	-
GCF_900130125.1	s__Bacteroides congonensis	77.7005	109	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_903181435.1	s__Bacteroides sp900765785	77.6657	120	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_000025985.1	s__Bacteroides fragilis	77.5526	137	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCF_000517545.1	s__Bacteroides reticulotermitis	77.3561	109	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_902364365.1	s__Bacteroides sp900556215	77.1591	119	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_000374585.1	s__Phocaeicola barnesiae	77.0559	52	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCA_900766195.1	s__Bacteroides sp900766195	76.9763	82	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556625.1	s__Bacteroides sp900556625	76.6709	66	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
GCF_016900355.1	s__Phocaeicola sp900551065	76.6117	53	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCA_900552645.1	s__Phocaeicola sp900552645	76.5821	51	642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:28:27,313] [INFO] GTDB search result was written to GCA_017986355.1_ASM1798635v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:28:27,314] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:28:27,330] [INFO] DFAST_QC result json was written to GCA_017986355.1_ASM1798635v1_genomic.fna/dqc_result.json
[2023-06-28 15:28:27,331] [INFO] DFAST_QC completed!
[2023-06-28 15:28:27,331] [INFO] Total running time: 0h1m11s